"John is in bed" can mean a few different things depending on the context:
John is ill: If the context involves discussing health or symptoms, it can imply that John is in bed because he's not feeling well.
John is lying on the bed: It can simply mean that John is physically on the bed, perhaps resting or relaxing.
John is asleep: In some contexts, it might imply that John is asleep or at least in bed intending to sleep.
Without additional context, it could mean any of these things. Adding more detail will help clarify the meaning if you need to be specific. For example:
"John is in bed because he's sick."
"John is lying in bed."
"John is in bed and probably asleep."